Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52G1Z

Calculation Name: 3MLR-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MLR

Chain ID: L

ChEMBL ID:

UniProt ID: P12490

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2121522.694935
FMO2-HF: Nuclear repulsion 2039683.477516
FMO2-HF: Total energy -81839.217418
FMO2-MP2: Total energy -82078.541236


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(L:1:SER)


Summations of interaction energy for fragment #1(L:1:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-19.817-30.33233.731-11.754-11.463-0.041
Interaction energy analysis for fragmet #1(L:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.078
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3L3ASP-1-0.843-0.9173.807-4.003-2.615-0.005-0.633-0.7510.000
4L4LEU0-0.055-0.0335.9560.6760.6760.0000.0000.0000.000
5L5THR00.0310.0108.3070.0820.0820.0000.0000.0000.000
6L6GLN00.027-0.01411.9580.0420.0420.0000.0000.0000.000
7L7PRO0-0.0190.01014.856-0.005-0.0050.0000.0000.0000.000
8L8PRO00.0860.05818.5280.0090.0090.0000.0000.0000.000
9L9SER0-0.027-0.01519.5510.0190.0190.0000.0000.0000.000
10L11VAL0-0.0030.00321.879-0.001-0.0010.0000.0000.0000.000
11L12SER0-0.0050.00124.5510.0080.0080.0000.0000.0000.000
12L13VAL00.0040.00328.293-0.001-0.0010.0000.0000.0000.000
13L14SER00.0250.01030.3980.0010.0010.0000.0000.0000.000
14L15PRO00.017-0.00233.529-0.001-0.0010.0000.0000.0000.000
15L16GLY0-0.026-0.00234.1950.0040.0040.0000.0000.0000.000
16L17GLN0-0.018-0.00132.9340.0030.0030.0000.0000.0000.000
17L18THR0-0.016-0.01927.7910.0000.0000.0000.0000.0000.000
18L19ALA00.0040.02525.801-0.002-0.0020.0000.0000.0000.000
19L20SER0-0.023-0.02023.1750.0000.0000.0000.0000.0000.000
20L21ILE00.0080.00917.721-0.006-0.0060.0000.0000.0000.000
21L22SER00.0250.01617.2450.0030.0030.0000.0000.0000.000
22L23CYS00.0010.00611.501-0.019-0.0190.0000.0000.0000.000
23L24SER0-0.031-0.00612.3320.0710.0710.0000.0000.0000.000
24L25GLY00.0900.0378.407-0.183-0.1830.0000.0000.0000.000
25L26ASP-1-0.901-0.9487.033-0.639-0.6390.0000.0000.0000.000
26L27LYS10.8330.9023.996-0.259-0.059-0.001-0.025-0.1750.000
27L28LEU00.0120.0208.1930.0590.0590.0000.0000.0000.000
28L29ASP-1-0.840-0.90310.285-0.046-0.0460.0000.0000.0000.000
29L30ASP-1-0.854-0.90710.9250.2120.2120.0000.0000.0000.000
30L31LYS10.7450.8687.320-0.300-0.3000.0000.0000.0000.000
31L32TYR0-0.066-0.03110.631-0.063-0.0630.0000.0000.0000.000
32L33VAL00.0120.00810.725-0.004-0.0040.0000.0000.0000.000
33L34SER0-0.048-0.02512.1230.0440.0440.0000.0000.0000.000
34L35TRP0-0.002-0.00413.361-0.061-0.0610.0000.0000.0000.000
35L36TYR0-0.014-0.01613.0430.0460.0460.0000.0000.0000.000
36L37TYR0-0.008-0.01317.445-0.016-0.0160.0000.0000.0000.000
37L38GLN00.006-0.01019.233-0.011-0.0110.0000.0000.0000.000
38L39ARG10.9140.96521.6760.0950.0950.0000.0000.0000.000
39L40PRO00.037-0.00824.8470.0010.0010.0000.0000.0000.000
40L41GLY0-0.0020.00325.0610.0100.0100.0000.0000.0000.000
41L42GLN0-0.045-0.00525.3410.0130.0130.0000.0000.0000.000
42L43SER00.0200.01222.137-0.011-0.0110.0000.0000.0000.000
43L44PRO0-0.006-0.01017.6270.0040.0040.0000.0000.0000.000
44L45VAL0-0.0120.00420.1010.0180.0180.0000.0000.0000.000
45L46LEU0-0.015-0.00116.990-0.015-0.0150.0000.0000.0000.000
46L47LEU0-0.018-0.01019.0530.0140.0140.0000.0000.0000.000
47L48MET0-0.029-0.01818.0850.0150.0150.0000.0000.0000.000
48L49TYR00.0340.01616.206-0.013-0.0130.0000.0000.0000.000
49L50GLN00.0270.01915.6720.0050.0050.0000.0000.0000.000
50L51ASP-1-0.780-0.87914.660-0.052-0.0520.0000.0000.0000.000
51L52PHE0-0.030-0.02316.909-0.013-0.0130.0000.0000.0000.000
52L53LYS10.8600.94319.9980.0210.0210.0000.0000.0000.000
53L54ARG10.9100.93821.0000.0510.0510.0000.0000.0000.000
54L55PRO0-0.0300.00321.5820.0100.0100.0000.0000.0000.000
55L56SER00.030-0.00524.110-0.001-0.0010.0000.0000.0000.000
56L57GLY0-0.015-0.01127.330-0.002-0.0020.0000.0000.0000.000
57L58ILE0-0.0180.01723.727-0.003-0.0030.0000.0000.0000.000
58L59PRO00.008-0.00227.0920.0050.0050.0000.0000.0000.000
59L60GLU-1-0.819-0.92127.917-0.051-0.0510.0000.0000.0000.000
60L61ARG10.7330.86529.0580.0830.0830.0000.0000.0000.000
61L62LEU00.0000.01522.690-0.006-0.0060.0000.0000.0000.000
62L63SER00.010-0.00724.1610.0060.0060.0000.0000.0000.000
63L64GLY00.0360.02120.025-0.014-0.0140.0000.0000.0000.000
64L65SER0-0.027-0.01719.4990.0150.0150.0000.0000.0000.000
65L66LYS10.8520.91013.1100.0290.0290.0000.0000.0000.000
66L67SER0-0.0100.00917.8270.0230.0230.0000.0000.0000.000
67L68GLY00.0400.02417.414-0.020-0.0200.0000.0000.0000.000
68L69LYS10.8040.87311.5080.1440.1440.0000.0000.0000.000
69L70THR00.0320.01012.883-0.074-0.0740.0000.0000.0000.000
70L71ALA00.0030.01813.7460.0450.0450.0000.0000.0000.000
71L72THR0-0.019-0.03715.476-0.037-0.0370.0000.0000.0000.000
72L73LEU0-0.0180.01418.4340.0240.0240.0000.0000.0000.000
73L74THR00.005-0.01920.088-0.006-0.0060.0000.0000.0000.000
74L75ILE00.0200.01423.3680.0100.0100.0000.0000.0000.000
75L76SER00.005-0.00126.3480.0020.0020.0000.0000.0000.000
76L77GLY00.025-0.00529.9420.0010.0010.0000.0000.0000.000
77L78THR0-0.068-0.03128.5450.0020.0020.0000.0000.0000.000
78L79GLN00.0390.01131.1260.0070.0070.0000.0000.0000.000
79L80SER00.0580.01331.310-0.004-0.0040.0000.0000.0000.000
80L81LEU0-0.025-0.01131.307-0.005-0.0050.0000.0000.0000.000
81L82ASP-1-0.707-0.79727.328-0.099-0.0990.0000.0000.0000.000
82L83GLU-1-0.866-0.90626.302-0.123-0.1230.0000.0000.0000.000
83L84GLY0-0.0180.00324.6380.0080.0080.0000.0000.0000.000
84L85ASP-1-0.805-0.85319.343-0.211-0.2110.0000.0000.0000.000
85L86TYR0-0.037-0.05218.5570.0190.0190.0000.0000.0000.000
86L87TYR00.0140.03013.360-0.024-0.0240.0000.0000.0000.000
87L89GLN00.018-0.0088.306-0.033-0.0330.0000.0000.0000.000
88L90ALA00.0410.0236.7920.1330.1330.0000.0000.0000.000
89L91TRP00.0140.0075.585-0.245-0.2450.0000.0000.0000.000
90L92ASP-1-0.760-0.8451.709-13.876-20.03518.991-7.297-5.535-0.041
91L93ALA0-0.025-0.0164.133-0.715-0.5670.000-0.051-0.0970.000
92L94SER00.0080.0063.9220.4070.450-0.001-0.005-0.0370.000
93L95THR00.0080.0086.6620.1350.1350.0000.0000.0000.000
94L95GLY00.0390.0349.6780.0650.0650.0000.0000.0000.000
95L95VAL00.0370.00610.495-0.130-0.1300.0000.0000.0000.000
96L95SER0-0.005-0.00113.001-0.056-0.0560.0000.0000.0000.000
97L95GLY0-0.0200.00114.173-0.052-0.0520.0000.0000.0000.000
98L95GLY0-0.003-0.01113.6430.0690.0690.0000.0000.0000.000
99L95GLY0-0.022-0.00313.8540.0020.0020.0000.0000.0000.000
100L96THR0-0.030-0.0239.0860.0640.0640.0000.0000.0000.000
101L97LYS10.9750.9974.620-3.452-3.410-0.001-0.004-0.0370.000
102L98LEU0-0.009-0.0176.540-0.033-0.0330.0000.0000.0000.000
103L99THR0-0.033-0.0262.6950.1011.1710.248-0.430-0.8880.002
104L100VAL0-0.0050.0124.820-0.175-0.105-0.001-0.002-0.0670.000
105L101LEU0-0.0220.0011.6842.516-4.83614.502-3.304-3.846-0.002
106L102PHE00.010-0.0225.0870.4700.505-0.001-0.003-0.0300.000
107L103GLY00.0480.0288.359-0.206-0.2060.0000.0000.0000.000
108L104ASP-1-0.923-0.96910.444-0.759-0.7590.0000.0000.0000.000
109L105GLY0-0.045-0.02012.9990.0770.0770.0000.0000.0000.000
110L106THR0-0.061-0.03915.687-0.003-0.0030.0000.0000.0000.000
111L106ARG10.8050.86218.8550.1990.1990.0000.0000.0000.000
112L107LEU0-0.053-0.03022.3110.0040.0040.0000.0000.0000.000
113L108THR0-0.025-0.02324.7940.0050.0050.0000.0000.0000.000
114L109VAL0-0.026-0.02528.4050.0010.0010.0000.0000.0000.000
115L110LEU0-0.017-0.02231.2750.0050.0050.0000.0000.0000.000
116L111GLY00.000-0.00534.3950.0040.0040.0000.0000.0000.000
117L112GLN0-0.079-0.03237.0580.0080.0080.0000.0000.0000.000
118L113PRO00.0270.00338.810-0.004-0.0040.0000.0000.0000.000
119L114LYS10.8710.94037.1410.0870.0870.0000.0000.0000.000
120L115ALA0-0.049-0.03139.7160.0040.0040.0000.0000.0000.000
121L116ALA00.0450.01840.284-0.004-0.0040.0000.0000.0000.000
122L117PRO0-0.0190.00939.2880.0020.0020.0000.0000.0000.000
123L118SER00.0050.00941.7060.0030.0030.0000.0000.0000.000
124L119VAL00.010-0.00941.624-0.002-0.0020.0000.0000.0000.000
125L120THR0-0.0050.00644.1860.0040.0040.0000.0000.0000.000
126L121LEU0-0.039-0.01543.115-0.002-0.0020.0000.0000.0000.000
127L122PHE0-0.003-0.00545.3280.0030.0030.0000.0000.0000.000
128L123PRO0-0.0040.00246.070-0.002-0.0020.0000.0000.0000.000
129L124PRO00.0400.02046.6490.0000.0000.0000.0000.0000.000
130L125SER0-0.017-0.01248.3400.0010.0010.0000.0000.0000.000
131L126SER00.010-0.02250.8990.0000.0000.0000.0000.0000.000
132L127GLU-1-0.839-0.90851.798-0.030-0.0300.0000.0000.0000.000
133L128GLU-1-0.792-0.87344.765-0.042-0.0420.0000.0000.0000.000
134L129LEU00.003-0.00249.4500.0010.0010.0000.0000.0000.000
135L130GLN0-0.072-0.02951.0450.0010.0010.0000.0000.0000.000
136L131ALA0-0.0220.00649.3080.0010.0010.0000.0000.0000.000
137L132ASN0-0.073-0.04248.9890.0000.0000.0000.0000.0000.000
138L133LYS10.8950.94641.7340.0390.0390.0000.0000.0000.000
139L134ALA00.003-0.00844.7370.0010.0010.0000.0000.0000.000
140L135THR0-0.022-0.03240.795-0.003-0.0030.0000.0000.0000.000
141L136LEU0-0.0490.00042.1880.0020.0020.0000.0000.0000.000
142L137VAL00.011-0.00441.104-0.004-0.0040.0000.0000.0000.000
143L138CYS0-0.083-0.01939.576-0.002-0.0020.0000.0000.0000.000
144L139LEU00.0010.00139.897-0.004-0.0040.0000.0000.0000.000
145L140ILE0-0.003-0.00436.7100.0020.0020.0000.0000.0000.000
146L141SER00.0340.00039.946-0.002-0.0020.0000.0000.0000.000
147L142ASP-1-0.810-0.89741.706-0.057-0.0570.0000.0000.0000.000
148L143PHE00.0250.03134.6920.0010.0010.0000.0000.0000.000
149L144TYR00.0260.02234.073-0.001-0.0010.0000.0000.0000.000
150L145PRO00.0720.01332.8330.0040.0040.0000.0000.0000.000
151L146GLY00.0070.00632.9670.0030.0030.0000.0000.0000.000
152L147ALA0-0.010-0.01129.880-0.007-0.0070.0000.0000.0000.000
153L148VAL0-0.009-0.00331.5920.0060.0060.0000.0000.0000.000
154L149THR00.0110.01829.835-0.008-0.0080.0000.0000.0000.000
155L150VAL00.008-0.00732.4440.0070.0070.0000.0000.0000.000
156L151ALA0-0.060-0.02233.755-0.006-0.0060.0000.0000.0000.000
157L152TRP00.0520.01635.9830.0070.0070.0000.0000.0000.000
158L153LYS10.8050.87338.3530.0640.0640.0000.0000.0000.000
159L154ALA00.0680.04441.1000.0020.0020.0000.0000.0000.000
160L155ASP-1-0.771-0.89043.419-0.043-0.0430.0000.0000.0000.000
161L156SER0-0.046-0.02944.659-0.001-0.0010.0000.0000.0000.000
162L157SER0-0.075-0.01740.990-0.003-0.0030.0000.0000.0000.000
163L158PRO00.027-0.00136.4020.0000.0000.0000.0000.0000.000
164L159VAL00.0100.01837.0190.0020.0020.0000.0000.0000.000
165L160LYS10.9480.95730.9200.1090.1090.0000.0000.0000.000
166L161ALA00.0080.01032.876-0.003-0.0030.0000.0000.0000.000
167L162GLY00.0550.02033.7570.0030.0030.0000.0000.0000.000
168L163VAL0-0.040-0.01332.9630.0030.0030.0000.0000.0000.000
169L164GLU-1-0.887-0.92930.008-0.105-0.1050.0000.0000.0000.000
170L165THR0-0.042-0.02231.3080.0070.0070.0000.0000.0000.000
171L166THR00.0110.01530.761-0.007-0.0070.0000.0000.0000.000
172L167THR0-0.017-0.01027.825-0.007-0.0070.0000.0000.0000.000
173L168PRO0-0.026-0.01730.3760.0060.0060.0000.0000.0000.000
174L169SER00.0030.01232.155-0.002-0.0020.0000.0000.0000.000
175L170LYS10.8760.94934.6190.0830.0830.0000.0000.0000.000
176L171GLN00.024-0.00536.8100.0020.0020.0000.0000.0000.000
177L172SER00.039-0.00140.5470.0000.0000.0000.0000.0000.000
178L173ASN0-0.021-0.00543.117-0.002-0.0020.0000.0000.0000.000
179L174ASN0-0.010-0.01539.818-0.002-0.0020.0000.0000.0000.000
180L175LYS10.8570.95838.8420.0570.0570.0000.0000.0000.000
181L176TYR0-0.004-0.01632.5190.0020.0020.0000.0000.0000.000
182L177ALA00.0210.01437.1370.0030.0030.0000.0000.0000.000
183L178ALA0-0.017-0.01834.964-0.005-0.0050.0000.0000.0000.000
184L179SER00.0150.02635.7890.0030.0030.0000.0000.0000.000
185L180SER0-0.003-0.01434.820-0.005-0.0050.0000.0000.0000.000
186L181TYR00.0110.00235.8840.0050.0050.0000.0000.0000.000
187L182LEU00.0260.02436.584-0.004-0.0040.0000.0000.0000.000
188L183SER0-0.029-0.00837.8300.0050.0050.0000.0000.0000.000
189L184LEU0-0.034-0.01839.726-0.002-0.0020.0000.0000.0000.000
190L185THR0-0.050-0.04442.4850.0010.0010.0000.0000.0000.000
191L186PRO00.0660.02245.185-0.001-0.0010.0000.0000.0000.000
192L187GLU-1-0.851-0.91348.185-0.032-0.0320.0000.0000.0000.000
193L188GLN0-0.0010.02241.3930.0000.0000.0000.0000.0000.000
194L189TRP00.0510.02746.820-0.001-0.0010.0000.0000.0000.000
195L190LYS10.9540.97148.0810.0280.0280.0000.0000.0000.000
196L191SER0-0.058-0.04549.2300.0010.0010.0000.0000.0000.000
197L192HIS0-0.101-0.03645.406-0.002-0.0020.0000.0000.0000.000
198L193LYS10.8850.92349.3950.0410.0410.0000.0000.0000.000
199L194SER0-0.046-0.02248.9000.0000.0000.0000.0000.0000.000
200L195TYR00.0580.02842.4980.0000.0000.0000.0000.0000.000
201L196SER00.001-0.01643.2230.0030.0030.0000.0000.0000.000
202L198GLN00.0300.00539.2880.0020.0020.0000.0000.0000.000
203L199VAL00.0170.00136.873-0.005-0.0050.0000.0000.0000.000
204L200THR0-0.020-0.01034.8280.0040.0040.0000.0000.0000.000
205L201HIS0-0.006-0.01435.089-0.004-0.0040.0000.0000.0000.000
206L202GLU-1-0.835-0.91333.620-0.101-0.1010.0000.0000.0000.000
207L203GLY0-0.007-0.00535.0030.0030.0030.0000.0000.0000.000
208L204SER0-0.0200.00736.3440.0050.0050.0000.0000.0000.000
209L205THR0-0.034-0.02238.579-0.002-0.0020.0000.0000.0000.000
210L206VAL0-0.0110.00540.7250.0040.0040.0000.0000.0000.000
211L207GLU-1-0.807-0.87241.947-0.066-0.0660.0000.0000.0000.000
212L208LYS10.8510.93043.9840.0550.0550.0000.0000.0000.000
213L209THR00.022-0.00345.237-0.002-0.0020.0000.0000.0000.000
214L210VAL0-0.027-0.00846.7860.0020.0020.0000.0000.0000.000
215L211ALA00.0500.00549.123-0.001-0.0010.0000.0000.0000.000
216L212PRO0-0.0210.00150.8880.0010.0010.0000.0000.0000.000
217L213THR0-0.0060.00953.2080.0010.0010.0000.0000.0000.000